And example CLI command and fix small bugs #91
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📝 WalkthroughWalkthroughThis update introduces new example files and scripts for molecular simulation workflows, adjusts parameter handling and output formatting in core modules, enhances test configuration and coverage, and revises documentation for clarity and current usage. The changes also improve compatibility with varying input conventions and simplify dependency management in the project configuration. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant ShellScript
participant dpti_CLI
participant LAMMPS
participant OutputFiles
User->>ShellScript: Run command.sh
ShellScript->>dpti_CLI: dpti generate NPT/NVT/HTI/TI input files
dpti_CLI->>OutputFiles: Write simulation input files
ShellScript->>LAMMPS: Submit simulation jobs
LAMMPS->>OutputFiles: Produce simulation results
ShellScript->>dpti_CLI: dpti extract/compute (e.g., Gibbs free energy)
dpti_CLI->>OutputFiles: Write processed results
Estimated code review effort🎯 4 (Complex) | ⏱️ ~40 minutes Possibly related PRs
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Actionable comments posted: 5
🔭 Outside diff range comments (1)
dpti/hti_water.py (1)
67-78:⚠️ Potential issueFallback may still return
None→ formatting crash
dict.get(... ) or dict.get(...)works, but if neither key exists the result isNone; the subsequentf"{sigma_oo:f}"will raiseTypeError: unsupported format string passed to NoneType.
Guard explicitly and fail fast with a helpful error.- sigma_oo = sparam.get("sigma_oo", None) or sparam.get("sigma_0_0") - sigma_oh = sparam.get("sigma_oh", None) or sparam.get("sigma_0_1") - sigma_hh = sparam.get("sigma_hh", None) or sparam.get("sigma_1_1") + try: + sigma_oo = sparam["sigma_oo"] if "sigma_oo" in sparam else sparam["sigma_0_0"] + sigma_oh = sparam["sigma_oh"] if "sigma_oh" in sparam else sparam["sigma_0_1"] + sigma_hh = sparam["sigma_hh"] if "sigma_hh" in sparam else sparam["sigma_1_1"] + except KeyError as exc: + raise KeyError(f"Missing LJ sigma parameter ({exc.args[0]}) in soft_param") from exc
🧹 Nitpick comments (7)
dpti/ti.py (1)
109-115: Duplicatethermo_modifyemission – collapse to one call
thermo_modify format float %20.6fis identical for the nvt and npt branches. You can emit it once after the ensemble-selection block to avoid drift if the format string changes again.- if ens == "nvt": - ret += "thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]\n" - ret += "thermo_modify format float %20.6f\n" - elif "npt" in ens: - ret += "thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]\n" - ret += "thermo_modify format float %20.6f\n" + ret += "thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]\n" + ret += "thermo_modify format float %20.6f\n" + if not (ens == "nvt" or "npt" in ens): + raise RuntimeError(f"unknown ensemble {ens}\n")Keeps behaviour identical, trims two lines, and eliminates future copy-paste edits.
dpti/equi.py (1)
134-148: Default-arg addition is 👍 but please adjust “npt” checkMaking
if_dump_avg_posioptional is a backward-compatible improvement – thanks.
Minor nit while you touch this area:
elif ens == "npt-iso" or ens == "npt":is slightly harder to read and can surprise with precedence in more complex expressions. A tuple-membership test is clearer and avoids the stray evaluation cost.- elif ens == "npt-iso" or ens == "npt": + elif ens in ("npt-iso", "npt"):🧰 Tools
🪛 Pylint (3.3.7)
[refactor] 139-139: Consider merging these comparisons with 'in' by using 'ens in ('npt-iso', 'npt')'. Use a set instead if elements are hashable.
(R1714)
tests/conftest.py (1)
6-15: Avoid hard-wiring project root intosys.pathat position 0Inserting the root at index 0 before std-lib & site-packages can shadow system modules and make import order subtly different from production.
Safer pattern:if project_root not in sys.path: sys.path.append(project_root) # append, don’t prependor rely on
pytest --pyargsbehaviour instead.The verbose
config.hook.pytest_terminal_summaryor the logging module.examples/Sn_High_Pressure/command.sh (4)
2-4: Quote arguments and use consistent flag styles in the NPT stage.Wrap JSON filenames and output paths in quotes to guard against spaces, and prefer long-form flags for clarity:
-dpti equi gen npt.json -e npt-xy -t 200 -p 20000 -o NPT_sim/ +dpti equi gen "npt.json" --ensemble "npt-xy" --temperature "200" --pressure "20000" --output "NPT_sim/"
7-9: Activate or clearly document directory navigation in the NVT stage.Commented
cdlines can confuse users. Either perform thecdand subsequent extract in a subshell or usepushd/popd, for example:mkdir -p NVT_sim && ( dpti equi gen "equi_settings.json" --ensemble "nvt" --temperature "200" --pressure "20000" --conf-npt "./NPT_sim/new_job/" --output "NVT_sim/" cd NVT_sim/new_job/ || exit 1 dpti equi extract . -o "nvt_last_dump.lmp" )
12-15: Remove or annotate commented alternative HTI commands.The commented
dpti hti_wateranddpti hti_icelines may mislead. Either delete them or add context:# For aqueous systems: # dpti hti_water gen hti_water.json -o HTI_water/ # For ice phases: # dpti hti_ice gen hti_ice.json --scheme three-step -o HTI_ice/
18-19: Quote file paths and unify flag naming in the TI stage.Consistently quote directory paths and use long-form flags to improve readability:
-dpti ti gen ti_settings.json -o TI_sim/ +dpti ti gen "ti_settings.json" --output "TI_sim/" -dpti ti compute ./TI_sim/new_job/ --hti ../HTI_sim/new_job/ +dpti ti compute "./TI_sim/new_job/" --hti "../HTI_sim/new_job/"
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📒 Files selected for processing (17)
dpti/__init__.py(1 hunks)dpti/equi.py(1 hunks)dpti/hti_liq.py(1 hunks)dpti/hti_water.py(1 hunks)dpti/ti.py(1 hunks)examples/Sn_High_Pressure/command.sh(1 hunks)examples/Sn_High_Pressure/conf.lmp(1 hunks)examples/Sn_High_Pressure/hti.json(1 hunks)tests/benchmark_gdi/deepmd/0/in.lammps(1 hunks)tests/benchmark_ti/path-p/in.lammps(1 hunks)tests/benchmark_ti/path-p/task.000006/in.lammps(1 hunks)tests/benchmark_ti/path-t/task.000006/in.lammps(1 hunks)tests/benchmark_ti_water/new_job/task.000003/in.lammps(1 hunks)tests/conftest.py(1 hunks)tests/graph.pb(1 hunks)tests/test_hti_ff_spring.py(1 hunks)tests/test_ti_gen_lammps_input.py(2 hunks)
🧰 Additional context used
🧬 Code Graph Analysis (1)
tests/test_hti_ff_spring.py (1)
dpti/hti.py (1)
_ff_spring(241-257)
🪛 Pylint (3.3.7)
dpti/__init__.py
[error] 15-15: Undefined variable name 'workflows' in all
(E0603)
🪛 Shellcheck (0.10.0)
examples/Sn_High_Pressure/command.sh
[error] 1-1: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.
(SC2148)
🔇 Additional comments (8)
examples/Sn_High_Pressure/conf.lmp (1)
1-1: Approve new LAMMPS config file.
The file correctly specifiesbeta.lmpas the input reference for the Sn_High_Pressure workflow.Please confirm that
conf.lmpis consumed by thecommand.shscript and documented in the example usage.tests/benchmark_gdi/deepmd/0/in.lammps (1)
27-29: Format update looks correctSwitching to
format float %20.6fmatches the current LAMMPS syntax and is already reflected in the generator.examples/Sn_High_Pressure/hti.json (1)
2-2: Confirm relative path forequi_conf
"equi_conf": "nvt_last_dump.lmp"assumes the file exists in the HTI job folder when the JSON is consumed. Double-check the preceding NVT step writes the dump there (or adjust to a relative/absolute path).tests/graph.pb (1)
5-5: Helpful download hintThanks for adding the compressed-model URL – improves reproducibility.
dpti/hti_liq.py (1)
361-367: Assignment now safely guarded – looks goodMoving
jdata["model"] = copied_modelinside theif model:block prevents aKeyErrorwhenmodelisNone. No further issues spotted.tests/benchmark_ti/path-p/task.000006/in.lammps (1)
29-29: Syntax now matches LAMMPS docs
thermo_modify format float %20.6fis the correct order (formatkeyword first). 👍tests/test_ti_gen_lammps_input.py (1)
65-65: Tests updated correctlyExpectations use the correct
thermo_modify format float %20.6fstring; aligns with generation logic.Also applies to: 131-131
tests/benchmark_ti_water/new_job/task.000003/in.lammps (1)
30-30: Thermo format string change LGTMSwitching to
format float %20.6fis consistent with other scripts and easier to read; no issues spotted.
| def test_spring_var_spring_multiple_element(self): | ||
| input = {"lamb": 0.20, "m_spring_k": [118.71, 207.2], "var_spring": False} | ||
| ret1 = textwrap.dedent( | ||
| """\ | ||
| group type_1 type 1 | ||
| group type_2 type 2 | ||
| fix l_spring_1 type_1 spring/self 1.1871000000e+02 | ||
| fix_modify l_spring_1 energy yes | ||
| fix l_spring_2 type_2 spring/self 2.0720000000e+02 | ||
| fix_modify l_spring_2 energy yes | ||
| variable l_spring equal f_l_spring_1+f_l_spring_2 | ||
| """ | ||
| ) | ||
| ret2 = dpti.hti._ff_spring(**input) | ||
| self.assertEqual(ret1, ret2) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Duplicate scenario & misleading test name
test_spring_var_spring_multiple_element sets var_spring=False, so it exercises the same code path already covered by test_spring_multiple_element.
Either:
- Rename to reflect it is a non-varying spring with a different λ, or
- Change
var_springtoTrueand update expected constants tok*(1-λ)so the varying-spring branch for multiple elements is actually tested.
Removing redundancy will keep the suite fast and intention-revealing.
🤖 Prompt for AI Agents
In tests/test_hti_ff_spring.py around lines 53 to 67, the test named
test_spring_var_spring_multiple_element sets var_spring to False, duplicating
the code path of test_spring_multiple_element. To fix this, either rename the
test to indicate it tests a non-varying spring with a different lambda value or
change var_spring to True and update the expected output constants to reflect
k*(1-lambda), ensuring the varying spring branch for multiple elements is
actually tested and removing redundancy.
| @@ -0,0 +1,19 @@ | |||
| # NPT | |||
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add a shebang and enable strict mode for portability and safety.
Without a shebang, the script may run under an unexpected shell. Enabling strict mode (-euo pipefail) ensures early failure on errors and prevents silent bugs.
Apply this diff:
+#!/usr/bin/env bash
+set -euo pipefail📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| # NPT | |
| #!/usr/bin/env bash | |
| set -euo pipefail | |
| # NPT |
🧰 Tools
🪛 Shellcheck (0.10.0)
[error] 1-1: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.
(SC2148)
🤖 Prompt for AI Agents
In examples/Sn_High_Pressure/command.sh at line 1, add a shebang line (e.g.,
#!/bin/bash) at the very top of the script to specify the shell interpreter.
Immediately after the shebang, enable strict mode by adding set -euo pipefail to
ensure the script exits on errors, treats unset variables as errors, and fails
on pipeline errors for better safety and portability.
There was a problem hiding this comment.
Actionable comments posted: 2
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (12)
dpti/hti.py(1 hunks)examples/water_SCAN/H2O-Phase-Diagram-model_compressed.pb(1 hunks)examples/water_SCAN/ice04/command.sh(1 hunks)examples/water_SCAN/ice04/conf.lmp(1 hunks)examples/water_SCAN/ice04/graph.pb(1 hunks)examples/water_SCAN/ice04/hti_ice.json(1 hunks)examples/water_SCAN/ice04/ice04.lmp(1 hunks)examples/water_SCAN/ice04/npt.json(1 hunks)examples/water_SCAN/ice04/nvt.json(1 hunks)examples/water_SCAN/ice04/path-p.json(1 hunks)examples/water_SCAN/ice04/path-t.json(1 hunks)tests/graph.pb(1 hunks)
✅ Files skipped from review due to trivial changes (9)
- examples/water_SCAN/ice04/graph.pb
- examples/water_SCAN/ice04/conf.lmp
- examples/water_SCAN/H2O-Phase-Diagram-model_compressed.pb
- examples/water_SCAN/ice04/ice04.lmp
- examples/water_SCAN/ice04/nvt.json
- examples/water_SCAN/ice04/npt.json
- examples/water_SCAN/ice04/path-p.json
- examples/water_SCAN/ice04/path-t.json
- examples/water_SCAN/ice04/hti_ice.json
🚧 Files skipped from review as they are similar to previous changes (1)
- tests/graph.pb
🧰 Additional context used
🧠 Learnings (3)
📓 Common learnings
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-08-04T02:54:28.797Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
dpti/hti.py (6)
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-08-04T02:54:28.797Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
examples/water_SCAN/ice04/command.sh (6)
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-08-04T02:54:28.797Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
🪛 Pylint (3.3.7)
dpti/hti.py
[refactor] 1336-1336: Consider using 'with' for resource-allocating operations
(R1732)
[refactor] 1338-1338: Consider using 'with' for resource-allocating operations
(R1732)
🪛 Shellcheck (0.10.0)
examples/water_SCAN/ice04/command.sh
[error] 1-1: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.
(SC2148)
🔇 Additional comments (1)
examples/water_SCAN/ice04/command.sh (1)
6-37: Excellent workflow documentation and command structure.The script provides a comprehensive and well-documented workflow for molecular dynamics simulations using the dpti tool. The step-by-step process from NPT/NVT equilibration through HTI and TI calculations is clearly structured and educational for users.
| # Try jdata.json first, then equi_settings.json for compatibility | ||
| try: | ||
| npt_in = json.load(open(os.path.join(npt, "jdata.json"))) | ||
| except FileNotFoundError: | ||
| npt_in = json.load(open(os.path.join(npt, "equi_settings.json"))) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve resource management while maintaining the fallback logic.
The fallback mechanism from jdata.json to equi_settings.json is a good improvement for compatibility. However, the file opening should use context managers to ensure proper resource cleanup.
Apply this diff to improve resource management:
- # Try jdata.json first, then equi_settings.json for compatibility
- try:
- npt_in = json.load(open(os.path.join(npt, "jdata.json")))
- except FileNotFoundError:
- npt_in = json.load(open(os.path.join(npt, "equi_settings.json")))
+ # Try jdata.json first, then equi_settings.json for compatibility
+ try:
+ with open(os.path.join(npt, "jdata.json")) as f:
+ npt_in = json.load(f)
+ except FileNotFoundError:
+ with open(os.path.join(npt, "equi_settings.json")) as f:
+ npt_in = json.load(f)📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| # Try jdata.json first, then equi_settings.json for compatibility | |
| try: | |
| npt_in = json.load(open(os.path.join(npt, "jdata.json"))) | |
| except FileNotFoundError: | |
| npt_in = json.load(open(os.path.join(npt, "equi_settings.json"))) | |
| # Try jdata.json first, then equi_settings.json for compatibility | |
| try: | |
| with open(os.path.join(npt, "jdata.json")) as f: | |
| npt_in = json.load(f) | |
| except FileNotFoundError: | |
| with open(os.path.join(npt, "equi_settings.json")) as f: | |
| npt_in = json.load(f) |
🧰 Tools
🪛 Pylint (3.3.7)
[refactor] 1336-1336: Consider using 'with' for resource-allocating operations
(R1732)
[refactor] 1338-1338: Consider using 'with' for resource-allocating operations
(R1732)
🤖 Prompt for AI Agents
In dpti/hti.py around lines 1334 to 1338, the code opens JSON files without
using context managers, which can lead to resource leaks. Refactor the file
opening statements to use 'with' blocks for both 'jdata.json' and
'equi_settings.json' to ensure files are properly closed after reading, while
preserving the fallback logic from 'jdata.json' to 'equi_settings.json'.
| # docker pull yfb222333/dpti-lammps-fep:latest | ||
| # docker run -it --gpus all dpti-lammps-fep:latest | ||
| # all in /opt/ | ||
| # all files in /opt/dpti/examples/water_SCAN/ice04/ | ||
|
|
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add shebang line for proper shell script execution.
The workflow documentation is excellent and provides clear guidance for users. However, the script should include a shebang line to specify the shell interpreter.
Add this line at the beginning of the file:
+#!/bin/bash
# docker pull yfb222333/dpti-lammps-fep:latest
# docker run -it --gpus all dpti-lammps-fep:latest
# all in /opt/
# all files in /opt/dpti/examples/water_SCAN/ice04/📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| # docker pull yfb222333/dpti-lammps-fep:latest | |
| # docker run -it --gpus all dpti-lammps-fep:latest | |
| # all in /opt/ | |
| # all files in /opt/dpti/examples/water_SCAN/ice04/ | |
| #!/bin/bash | |
| # docker pull yfb222333/dpti-lammps-fep:latest | |
| # docker run -it --gpus all dpti-lammps-fep:latest | |
| # all in /opt/ | |
| # all files in /opt/dpti/examples/water_SCAN/ice04/ |
🧰 Tools
🪛 Shellcheck (0.10.0)
[error] 1-1: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.
(SC2148)
🤖 Prompt for AI Agents
In examples/water_SCAN/ice04/command.sh at the beginning of the file, add a
shebang line such as #!/bin/bash to specify the shell interpreter for proper
script execution.
There was a problem hiding this comment.
Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (1)
examples/download_models.sh(1 hunks)
🧰 Additional context used
🧠 Learnings (1)
📓 Common learnings
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-08-04T02:54:28.797Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
🪛 Shellcheck (0.10.0)
examples/download_models.sh
[error] 1-1: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.
(SC2148)
🔇 Additional comments (1)
examples/download_models.sh (1)
3-3: Verify URL spelling and remove superfluous whitespaceThe path segment
Phase-Dirgramlooks like a typo of “Diagram”; a broken URL will silently create an HTML error page saved asH2O-Phase-Diagram-model_compressed.pb.
Also there’s an extra space afterwget.-wget https://huggingface.co/Felix5572/Water-Ice-SCAN-Phase-Dirgram/resolve/main/graph.pb -O H2O-Phase-Diagram-model_compressed.pb +wget https://huggingface.co/Felix5572/Water-Ice-SCAN-Phase-Diagram/resolve/main/graph.pb -O H2O-Phase-Diagram-model_compressed.pbPlease confirm the correct repository slug before merging.
| @@ -0,0 +1,3 @@ | |||
| wget https://huggingface.co/Felix5572/Sn-SCAN-Compressed/resolve/main/graph.pb -O Sn_SCAN_compressed.pb | |||
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add she-bang and fail-fast options for predictable execution
Without a she-bang the script’s interpreter is ambiguous (SC2148).
Insert a standard header and strict mode so any network/download failure aborts the script immediately.
+#!/usr/bin/env bash
+# Download compressed DeepPot models required by example workflows
+set -euo pipefail
+
wget https://huggingface.co/Felix5572/Sn-SCAN-Compressed/resolve/main/graph.pb -O Sn_SCAN_compressed.pb📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| wget https://huggingface.co/Felix5572/Sn-SCAN-Compressed/resolve/main/graph.pb -O Sn_SCAN_compressed.pb | |
| #!/usr/bin/env bash | |
| # Download compressed DeepPot models required by example workflows | |
| set -euo pipefail | |
| wget https://huggingface.co/Felix5572/Sn-SCAN-Compressed/resolve/main/graph.pb -O Sn_SCAN_compressed.pb |
🧰 Tools
🪛 Shellcheck (0.10.0)
[error] 1-1: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.
(SC2148)
🤖 Prompt for AI Agents
In examples/download_models.sh at line 1, add a she-bang line (e.g.,
#!/bin/bash) at the top to specify the script interpreter explicitly. Also,
enable fail-fast behavior by adding set -e to the script so it exits immediately
on any command failure, ensuring predictable execution and proper error handling
during the download process.
There was a problem hiding this comment.
Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (1)
pyproject.toml(1 hunks)
🧰 Additional context used
🧠 Learnings (1)
📓 Common learnings
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-08-04T02:54:28.797Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file.
🔇 Additional comments (1)
pyproject.toml (1)
23-23: Airflow removed from hard dependencies – confirm no runtime imports remain
apache-airflowis now merely commented out. If any module still executesimport airflow(directly or transitively), end-users will hitModuleNotFoundError.
• Grep the codebase for “airflow” and either (a) move it to an[project.optional-dependencies] airflow = [...]extra or (b) re-add it as a required dep.
| "dargs", | ||
| "dpdispatcher >= 0.3", | ||
| "sqlalchemy >=1.4.28,<2.0", | ||
| "sqlalchemy", |
There was a problem hiding this comment.
💡 Verification agent
🧩 Analysis chain
Unpinning sqlalchemy exposes you to breaking API changes in 2.x
The code previously limited SQLAlchemy to <2.0; lifting that guard allows automatic upgrade to 2.x, whose ORM and core APIs contain several backwards-incompatible changes (e.g., engine.execute removal). Unless the codebase has already been ported, keep the upper bound.
- "sqlalchemy",
+ "sqlalchemy >=1.4.28, <2.0",To confirm whether we’ve unbounded SQLAlchemy and if there are any calls that would break under 2.x, let’s check the dependency spec and look for engine.execute usages:
🏁 Script executed:
#!/bin/bash
# Show how SQLAlchemy is currently specified
grep -n "sqlalchemy" pyproject.toml
# Find any direct calls to the removed Engine.execute API
grep -R "engine.execute" -n .Length of output: 249
Pin SQLAlchemy to <2.0 to avoid unintended 2.x breakages
We’ve confirmed that pyproject.toml currently has an unbounded SQLAlchemy dependency and there are no obvious calls to the removed Engine.execute, but SQLAlchemy 2.x introduces several incompatible changes beyond that (ORM query API, typing, deprecations, etc.). Unless the entire codebase has been audited and updated for 2.0, it’s safest to restore an upper bound:
--- pyproject.toml
@@ lines 29
- "sqlalchemy",
+ "sqlalchemy >=1.4.28, <2.0",Please pin the version until you complete a full 2.0 compatibility pass.
🤖 Prompt for AI Agents
In pyproject.toml at line 29, the SQLAlchemy dependency is currently unbounded,
which risks compatibility issues with SQLAlchemy 2.x. To fix this, modify the
dependency specification to pin SQLAlchemy to a version less than 2.0 by adding
an upper bound constraint like "<2.0" to the version specifier. This ensures the
project uses a compatible version until a full upgrade to 2.0 is completed.
for more information, see https://pre-commit.ci
There was a problem hiding this comment.
Actionable comments posted: 2
🧹 Nitpick comments (8)
README.md (4)
55-58: Fix multiple typos in introduction paragraph
anaylze,scirpts, and a few grammar issues weaken credibility.-At first, dpti is a collection of python scripts to generate LAMMPS input scripts and to anaylze results from LAMMPS logs.<br /> -<br />In dpti, there are many MD simulations tasks and scripts need to be run sequentially or concurrently. Before and after these MD simulation tasks, we may run a lot of MD scirpts to prepare the input files or analyze the logs to extract the useful data.<br /> +Initially, **dpti** was a collection of Python scripts that generated LAMMPS inputs and analysed the resulting logs.<br /> +<br />In **dpti**, many MD-simulation tasks must be run sequentially or concurrently. Before and after these tasks we often run helper scripts to prepare input files or analyse logs and extract useful data.<br />
60-82: Add language identifier to fenced block & fix spelling
MD040is triggered here and “usefule” is misspelled.-``` +dpti directory tree +```text dpti/ # main directory for dpti python modules -dpti/lib/ usefule libs for numberical integration and analysis, free energy calculation, etc. +dpti/lib/ useful libs for numerical integration and analysis, free-energy calculation, etc. # example dir structure ...--- `98-128`: **Mark example script blocks as Bash for syntax highlighting** ```diff -``` +# Navigate to the example directory +```bash ... -``` +# Common dpti one-liners +```bash ...--- `181-184`: **Specify language for single-line CLI snippet** ```diff -``` +```bash dpti ti compute ./TI_sim/new_job/ --hti ../HTI_sim/new_job/</blockquote></details> <details> <summary>workflow/README.md (4)</summary><blockquote> `66-71`: **Add correct language tag for airflow config snippet** ```diff -``` +```ini # sql_alchemy_conn = sqlite:////home/fengbo/airflow/airflow.db # sql_alchemy_conn = postgres://airflow:airflow@localhost:5432/airflow sql_alchemy_conn = postgresql+psycopg2://<user>:<password>@<host>:<port>/<db_name>--- `75-81`: **Fenced block missing language identifier** Mark the database-reset commands as bash to satisfy `MD040`. ```diff -``` +```bash # reset db airflow db init ...--- `165-166`: **Grammar: remove “and etc.”** ```diff -**Parameters:** Given temperature(or the range), Given pressure(or therange), force field,Lammps simulation ensemble and etc. +**Parameters:** Temperature (or range), pressure (or range), force field, LAMMPS simulation ensemble, etc.
178-226: Duplicate section – please deduplicate to reduce maintenance costLines 178-226 repeat the “For airflow workflow / TI_Workflow” description almost verbatim from 125-173. Recommend deleting one copy to avoid divergence in future edits.
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📒 Files selected for processing (3)
README.md(9 hunks)tests/benchmark_ti/path-t/task.000006/in.lammps(1 hunks)workflow/README.md(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- tests/benchmark_ti/path-t/task.000006/in.lammps
🧰 Additional context used
🧠 Learnings (2)
📓 Common learnings
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-08-04T02:54:28.797Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:57-59
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_header` function in `dpti/equi.py` now includes a `custom_variables` parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: deepmodeling/dpti#70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The `gen_equi_force_field` function in `dpti/equi.py` now includes an `append` parameter to append a user-defined string to the model file name in the `pair_style` line of the LAMMPS input file.
README.md (6)
Learnt from: Yi-FanLi
PR: #70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The gen_equi_force_field function in dpti/equi.py now includes an append parameter to append a user-defined string to the model file name in the pair_style line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: #70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The gen_equi_force_field function in dpti/equi.py now includes an append parameter to append a user-defined string to the model file name in the pair_style line of the LAMMPS input file.
Learnt from: Yi-FanLi
PR: #70
File: dpti/equi.py:179-180
Timestamp: 2024-08-04T02:53:14.784Z
Learning: The gen_equi_header function in dpti/equi.py now includes a custom_variables parameter to handle custom variables in the LAMMPS input file.
Learnt from: Yi-FanLi
PR: #70
File: dpti/equi.py:179-180
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The gen_equi_header function in dpti/equi.py now includes a custom_variables parameter to handle custom variables in the LAMMPS input file.
Learnt from: Yi-FanLi
PR: #70
File: dpti/equi.py:57-59
Timestamp: 2024-10-08T15:32:11.479Z
Learning: The gen_equi_header function in dpti/equi.py now includes a custom_variables parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
Learnt from: Yi-FanLi
PR: #70
File: dpti/equi.py:57-59
Timestamp: 2024-08-04T02:54:28.797Z
Learning: The gen_equi_header function in dpti/equi.py now includes a custom_variables parameter to handle custom variables in the LAMMPS input file. Ensure that unit tests cover this functionality.
🪛 markdownlint-cli2 (0.17.2)
README.md
20-20: Bare URL used
(MD034, no-bare-urls)
23-23: Bare URL used
(MD034, no-bare-urls)
66-66: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
98-98: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
108-108: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
182-182: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
225-225: Bare URL used
(MD034, no-bare-urls)
307-307: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
workflow/README.md
54-54: Multiple spaces after hash on atx style heading
(MD019, no-multiple-space-atx)
66-66: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
75-75: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
99-99: Spaces inside code span elements
(MD038, no-space-in-code)
114-114: Link fragments should be valid
(MD051, link-fragments)
114-114: Link fragments should be valid
(MD051, link-fragments)
120-120: Link fragments should be valid
(MD051, link-fragments)
122-122: Link fragments should be valid
(MD051, link-fragments)
125-125: Trailing punctuation in heading
Punctuation: ':'
(MD026, no-trailing-punctuation)
141-141: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
147-147: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
153-153: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
174-174: Trailing punctuation in heading
Punctuation: '.'
(MD026, no-trailing-punctuation)
178-178: Multiple headings with the same content
(MD024, no-duplicate-heading)
178-178: Trailing punctuation in heading
Punctuation: ':'
(MD026, no-trailing-punctuation)
194-194: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
200-200: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
206-206: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
🪛 LanguageTool
workflow/README.md
[style] ~165-~165: Write the name of the item after ‘and’ or use only “etc”.
Context: ... force field,Lammps simulation ensemble and etc. we implement a workflow called TI_tas...
(AND_ETC)
[style] ~218-~218: Write the name of the item after ‘and’ or use only “etc”.
Context: ... force field,Lammps simulation ensemble and etc. we implement a workflow called TI_tas...
(AND_ETC)
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)
- GitHub Check: build (3.9)
| useful links: | ||
|
|
||
| github README.md: [https://github.com/deepmodeling/dpti/README.md](https://github.com/deepmodeling/dpti/README.md) | ||
|
|
||
| some discussion notes: [https://www.yuque.com/dpti/manual/ilzmlb](https://www.yuque.com/dpti/manual/ilzmlb) | ||
| On Bohrium Platform: | ||
| Bohrium notebook: | ||
| The basic usage of dpti, commands and examples: | ||
| https://www.bohrium.com/notebooks/82544159178 | ||
|
|
||
| intruction to free energy calculation: | ||
| Demo site: | ||
| https://www.bohrium.com/apps/dpti | ||
|
|
||
|
|
||
| intruction to free energy calculation via thermodynamic integration method: | ||
| [https://nb.bohrium.dp.tech/detail/18465833825](https://nb.bohrium.dp.tech/detail/18465833825) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Standardise “Useful links” section & avoid bare URLs
Convert the free-form list into a proper Markdown heading + bullet list, fix the typo “intruction”, and wrap raw URLs with angle brackets to silence MD034.
- useful links:
- github README.md: [https://github.com/deepmodeling/dpti/README.md](https://github.com/deepmodeling/dpti/README.md)
- On Bohrium Platform:
- Bohrium notebook:
- The basic usage of dpti, commands and examples:
- https://www.bohrium.com/notebooks/82544159178
- Demo site:
- https://www.bohrium.com/apps/dpti
- intruction to free energy calculation via thermodynamic integration method:
- [https://nb.bohrium.dp.tech/detail/18465833825](https://nb.bohrium.dp.tech/detail/18465833825)
+ ## Useful links
+ - GitHub README <https://github.com/deepmodeling/dpti/README.md>
+ - Bohrium notebook – basic usage & examples <https://www.bohrium.com/notebooks/82544159178>
+ - Online demo <https://www.bohrium.com/apps/dpti>
+ - Introduction to thermodynamic-integration free-energy calculation <https://nb.bohrium.dp.tech/detail/18465833825>📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| useful links: | |
| github README.md: [https://github.com/deepmodeling/dpti/README.md](https://github.com/deepmodeling/dpti/README.md) | |
| some discussion notes: [https://www.yuque.com/dpti/manual/ilzmlb](https://www.yuque.com/dpti/manual/ilzmlb) | |
| On Bohrium Platform: | |
| Bohrium notebook: | |
| The basic usage of dpti, commands and examples: | |
| https://www.bohrium.com/notebooks/82544159178 | |
| intruction to free energy calculation: | |
| Demo site: | |
| https://www.bohrium.com/apps/dpti | |
| intruction to free energy calculation via thermodynamic integration method: | |
| [https://nb.bohrium.dp.tech/detail/18465833825](https://nb.bohrium.dp.tech/detail/18465833825) | |
| ## Useful links | |
| - GitHub README <https://github.com/deepmodeling/dpti/README.md> | |
| - Bohrium notebook – basic usage & examples <https://www.bohrium.com/notebooks/82544159178> | |
| - Online demo <https://www.bohrium.com/apps/dpti> | |
| - Introduction to thermodynamic-integration free-energy calculation <https://nb.bohrium.dp.tech/detail/18465833825> |
🧰 Tools
🪛 markdownlint-cli2 (0.17.2)
20-20: Bare URL used
(MD034, no-bare-urls)
23-23: Bare URL used
(MD034, no-bare-urls)
🤖 Prompt for AI Agents
In README.md around lines 13 to 27, standardize the "Useful links" section by
adding a proper Markdown heading, converting the list into bullet points,
correcting the typo "intruction" to "instruction," and wrapping all raw URLs in
angle brackets to prevent Markdown linting errors related to bare URLs.
| ### TI_Workflow | ||
| We implement a workflow de | ||
| implemented at `workflow/DpFreeEnergy.py` | ||
|
|
There was a problem hiding this comment.
Incomplete sentence – clarify TI workflow description
-### TI_Workflow
-We implement a workflow de
-implemented at `workflow/DpFreeEnergy.py`
+### TI workflow
+The DAG `workflow/DpFreeEnergy.py` automates NPT → NVT → HTI → TI to obtain free-energy data.📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| ### TI_Workflow | |
| We implement a workflow de | |
| implemented at `workflow/DpFreeEnergy.py` | |
| ### TI workflow | |
| The DAG `workflow/DpFreeEnergy.py` automates NPT → NVT → HTI → TI to obtain free‐energy data. |
🤖 Prompt for AI Agents
In workflow/README.md around lines 136 to 139, the description of the
TI_Workflow is incomplete and unclear. Complete the sentence to clearly explain
what the TI_Workflow is and how it is implemented, ensuring the explanation is
concise and informative for readers.
1 participant
Summary by CodeRabbit
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Documentation
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